SMTL ID : 1e7s.1

GDP 4-keto-6-deoxy-D-mannose epimerase reductase K140R

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 22 residues within 4Å: Chain A: G.10, R.12, G.13, M.14, V.15, R.36, L.39, N.40, L.41, L.42, A.62, A.63, A.64, V.66, G.67, G.68, I.86, L.166, D.171, N.177, H.179 Ligands: UVW.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:M.14, A:V.15, A:N.40, A:L.41, A:L.42, A:A.64, A:G.68, A:N.177, A:H.179 Water bridges: A:R.12, A:G.13, A:G.16, A:R.36, A:R.36, A:R.36, A:R.36, A:A.62, A:R.140, A:R.140, A:R.140, A:L.166, A:L.166, A:L.166 Salt bridges: A:R.36 NAP.7: 22 residues within 4Å: Chain B: G.10, R.12, G.13, M.14, V.15, R.36, L.39, N.40, L.41, L.42, A.62, A.63, A.64, V.66, G.67, G.68, I.86, L.166, D.171, N.177, H.179 Ligands: UVW.8 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:M.14, B:V.15, B:N.40, B:L.41, B:L.42, B:A.64, B:G.68, B:N.177, B:H.179, B:H.179 Water bridges: B:R.12, B:G.13, B:G.16, B:R.36, B:R.36, B:R.36, B:R.36, B:A.62, B:R.140, B:R.140, B:R.140, B:L.166, B:L.166, B:L.166 Salt bridges: B:R.36

2 x UVW: ACETYLPHOSPHATE(Non-covalent)

UVW.2: 7 residues within 4Å: Chain A: G.67, G.68, I.69, V.70, A.71, S.178 Ligands: NAP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.68, A:V.70, A:A.71 UVW.8: 7 residues within 4Å: Chain B: G.67, G.68, I.69, V.70, A.71, S.178 Ligands: NAP.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.68, B:V.70, B:A.71

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: H.11, R.12, R.20, T.35 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.11, A:R.20 Salt bridges: A:H.11, A:R.12, A:R.20 SO4.4: 3 residues within 4Å: Chain A: R.152, P.238, M.239 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.152, A:R.152 Salt bridges: A:R.152 SO4.6: 2 residues within 4Å: Chain A: R.209, K.283 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.209, A:R.209, A:T.280 Salt bridges: A:R.209, A:K.283 SO4.9: 4 residues within 4Å: Chain B: H.11, R.12, R.20, T.35 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.11, B:R.20 Salt bridges: B:H.11, B:R.12, B:R.20 SO4.10: 3 residues within 4Å: Chain B: R.152, P.238, M.239 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.152, B:R.152 Salt bridges: B:R.152 SO4.12: 2 residues within 4Å: Chain B: R.209, K.283 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.209, B:R.209, B:T.280 Salt bridges: B:R.209, B:K.283

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 4 residues within 4Å: Chain A: S.17, R.21, H.170, W.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.21 Water bridges: A:R.21, A:R.21 TRS.11: 4 residues within 4Å: Chain B: S.17, R.21, H.170, W.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.21 Water bridges: B:R.21, B:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosano, C. et al., Probing the Catalytic Mechanism of Gdp-4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase by Kinetic and Crystallographic Characterization of Site-Specific Mutants. J.Mol.Biol. (2000)

Release Date

2000-10-18

Peptides

GDP-FUCOSE SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GDP-FUCOSE SYNTHETASE